Table 5

Spearman's rank correlations of heterozygosity with microsatellite sequence properties and measures of variation across individuals

1 STR region

2 STR regions

3 STR regions




Di

Tri

Tetra

Di

Tri

Tetra

Tetra

Number of loci

30

133

325

10

15

97

12


    Sequence properties

G/C content of flanking sequence

0.247

0.037

-0.034

0.237

0.291

0.142

0.035

Number of nucleotides separating STR regions

-

-

-

0.140

0.568

0.032

0.252

    Measures of variation across individuals

Number of distinct alleles

0.424

0.431

0.517

0.628

0.497

0.596

0.644

Variance in number of repeats

0.325

0.502

0.800

0.636

0.750

0.779

0.846

Range of number of repeats

0.151

0.326

0.492

0.646

0.304

0.672

0.681

Mean PCR fragment size

0.040

0.007

-0.016

-0152

0.571

0.126

0.308

Mean number of repeats

0.564

0.239

0.134

0.455

0.018

0.388

0.503

Maximum number of repeats

0.465

0.228

0.384

0.669

0.235

0.562

0.706

Minimum number of repeats

0.335

-0.036

-0.044

0.049

-0.079

-0.036

0.385


Spearman's rank correlation coefficients (ρ) are shown for comparisons of microsatellite heterozygosity with continuous microsatellite sequence properties and with measures of variation across individuals in the HGDP-CEPH data set. Microsatellites were classified by the number of separate STR regions embedded in their sequence and by their repeat unit size. Hyphens indicate comparisons that were not evaluated. For three STR regions, no comparisons were performed for di-nucleotide and tri-nucleotide loci because of small sample size (3 and 2, respectively). Correlations with P < 0.05 are highlighted in bold.

Pemberton et al. BMC Genomics 2009 10:612   doi:10.1186/1471-2164-10-612

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